160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Li, Isaac T S ^a   Shum, Warren ^b   Truong, Kevin ^a,b  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATION TIME; FIELD PROPAGATION; GENOMIC DATABASE; LOCAL ALIGNMENT; SEARCHING SEQUENCE; SMITH-WATERMAN; SMITH-WATERMAN ALGORITHM; SOFTWARE IMPLEMENTATION;

ALGORITHMS; FIELD PROGRAMMABLE GATE ARRAYS (FPGA); HARDWARE; SEARCH ENGINES;

MATRIX ALGEBRA;

ARTICLE; COMPUTER PROGRAM; COMPUTER SYSTEM; GENE FUNCTION; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC DATABASE; MATHEMATICAL COMPUTING; SCORING SYSTEM; ALGORITHM; DNA SEQUENCE; EQUIPMENT; EQUIPMENT DESIGN; INSTRUMENTATION; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SIGNAL PROCESSING;

ALGORITHMS; BASE SEQUENCE; EQUIPMENT DESIGN; EQUIPMENT FAILURE ANALYSIS; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SIGNAL PROCESSING, COMPUTER-ASSISTED;

EID: 34347225963     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-185     Document Type: Article

References (10)

1. Smith TF Waterman MS Identification of common molecular subsequences J Mol Biol 1981 147 1 195-197 7265238
2. Page RD GeneTree: Comparing gene and species phylogenies using reconciled trees Bioinformatics 1998 14 9 819-820 9918954
3. Lipman DJ Pearson WR Rapid and sensitive protein similarity searches Science 1985 227 4693 1435-1441 2983426
4. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990 215 3 403-410 2231712
5. Hughey R Parallel hardware for sequence comparison and alignment Comput Appl Biosci 1996 12 6 473-479 9021265
6. Chow ET Peterson JC Waterman MS Hunkapiller T Zimmermann BA A systolic array processor for biological information signal processing Proceedings of the 5th international conference on Supercomputing 1991 216-223
7. Borah M Bajwa RS Hannenhalli S Irwin MJ A SIMD solution to the sequence comparison problem on the MGAP Proceedings of Application Specific Array Processors 1994 336-345
8. Rognes T Seeberg E Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors Bioinformatics 2000 16 8 699-706 11099256
9. Giegerich R A systematic approach to dynamic programming in bioinformatics Bioinformatics 2000 16 8 665-677 11099253
10. Farrar M Striped Smith-Waterman speeds database searches six times over other SIMD implementations Bioinformatics 2007 23 2 156-161 17110365